A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
/project/xinhe/xsun/camseq/data_multicelltypes/merged_workspace/reports_all
General Statistics
| Sample Name | Unique Reads | Pass Dedup | % Aligned | Trimmed bases |
|---|---|---|---|---|
| S1.genome | 46.4M | 63.4% | 98.9% | 36.9% |
| S2.genome | 61.0M | 68.4% | 99.2% | 40.9% |
| S3.genome | 81.4M | 59.0% | 99.1% | 38.0% |
| S4.genome | 62.9M | 57.1% | 99.0% | 36.1% |
| S5.genome | 73.2M | 62.9% | 99.1% | 37.9% |
| S6.genome | 32.4M | 38.4% | 98.8% | 37.3% |
| S7.genome | 58.6M | 60.9% | 99.0% | 34.9% |
| S8.genome | 55.3M | 77.8% | 99.0% | 37.8% |
| S9.genome | 57.2M | 74.5% | 98.9% | 37.0% |
| S10.genome | 56.0M | 74.8% | 99.0% | 37.3% |
| S11.genome | 17.2M | 23.9% | 29.0% | 71.4% |
| S12.genome | 22.2M | 33.4% | 26.0% | 68.5% |
| S13.genome | 17.2M | 26.7% | 28.6% | 71.4% |
| S14.genome | 26.4M | 31.0% | 28.5% | 71.1% |
| S15.genome | 19.0M | 29.4% | 25.8% | 69.3% |
| S16.genome | 9.8M | 53.1% | 23.8% | 80.7% |
| S17.genome | 27.3M | 25.0% | 30.8% | 72.6% |
| S18.genome | 12.4M | 18.4% | 27.3% | 69.2% |
| S19.genome | 9.7M | 16.2% | 26.1% | 69.8% |
| S20.genome | 18.3M | 34.4% | 26.5% | 69.9% |
UMICollapse
Algorithms for efficiently collapsing reads with Unique Molecular Identifiers.URL: https://github.com/Daniel-Liu-c0deb0t/UMICollapseDOI: 10.7717/peerj.8275
Deduplicated Reads
UMI Stats
Statistics from running umicollapse
- Positions Dedup: Total number of positions deduplicated
- Mean #UMI: Mean number of unique UMIs per position
- Max #UMI: Max number of unique UMIs per position
- Discarded reads: Discarded unmapped, unpaired, or chimeric reads
HISAT2
Maps DNA or RNA reads against a genome or a population of genomes.URL: https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4
Please note that single mate alignment counts are halved to tally with pair counts properly.
Cutadapt
4.9
Finds and removes adapter sequences, primers, poly-A tails, and other types of unwanted sequences.URL: https://cutadapt.readthedocs.ioDOI: 10.14806/ej.17.1.200
Filtered Reads
This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Software | Version |
|---|---|
| Cutadapt | 4.9 |